Open Hoberti opened 2 years ago
Hello,
Which Braker and Augustus versions are you using?
braker.pl --version
braker.pl version 2.1.5
augustus --version
AUGUSTUS (3.4.0) is a gene prediction tool.
Sources and documentation at https://github.com/Gaius-Augustus/Augustus
In my /home/ubuntu/anaconda3/envs/fungap/bin/getAnnoFastaFromJoingenes.py
script, there's no Bio.Alphabet
.
Its header looks like this:
#!/usr/bin/env python3
# Author: Katharina J. Hoff
# E-Mail: katharina.hoff@uni-greifswald.de
# Last modified on August 26th 2019
#
# This Python script extracts CDS features from a GTF file, excises
# corresponding sequence windows from a genome FASTA file, stitches the
# codingseq parts together, adds letters N at the ends if bases are
# annotated as missing by frame in the GTF file, makes reverse complement
# if required, and translates to protein sequence.
# Output files are:
# * file with protein sequences in FASTA format,
# * file with coding squences in FASTA format
# The script automatically checks for in-frame stop codons and prints a
# warning to STDOUT if such genes are in the GTF-file. The IDs of bad genes
# are printed to a file bad_genes.lst. Option -s allows to exclude bad genes
# from the FASTA output file, automatically.
# Beware: the script assumes that the gtf input file is sorted by coordinates!
Hi,
I find this when I run run_braker
getAnnoFastaFromJoingenes.py -g maker_out/masked_assembly.fasta.adjusted -o braker_out/308/braker_308 -t 1 -3 braker_out/308/braker_308.gff3
anaconda3/envs/fungap/bin/getAnnoFastaFromJoingenes.py Traceback (most recent call last): File "/anaconda3/envs/FUNGAP/bin/getAnnoFastaFromJoingenes.py", line 35, in
from Bio.Alphabet import generic_dna, generic_protein
File "anaconda3/envs/FUNGAP/lib/python3.8/site-packages/Bio/Alphabet/init.py", line 20, in
raise ImportError(
ImportError: Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the
molecule_type
as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information.During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "anaconda3/envs/FUNGAP/bin/getAnnoFastaFromJoingenes.py", line 39, in
raise ImportError(
ImportError: Failed to import biophython modules. Try installing with "pip3 install biopython"
I find that biopython==1.79 has no more the Bio.Alphabet module, this could easily solucionated when installing biopython with pip: pip install biopython==1.75
Is this correct?
Héctor